A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies

Duong, Van An, Enkhbayar, Altai, Bhasin, Nobel, Senavirathna, Lakmini, Preisner, Eva C., Hoffman, Kristi L., Shukla, Richa, Jenq, Robert R., Cheng, Kai, Bronner, Mary P., Figeys, Daniel, Britton, Robert A., Pan, Sheng and Chen, Ru (2024) A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies. Proteomics, 24 (21-22). ISSN 1615-9853

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Abstract

The human gut microbiome plays a vital role in preserving individual health and is intricately involved in essential functions. Imbalances or dysbiosis within the microbiome can significantly impact human health and are associated with many diseases. Several metaproteomics platforms are currently available to study microbial proteins within complex microbial communities. In this study, we attempted to develop an integrated pipeline to provide deeper insights into both the taxonomic and functional aspects of the cultivated human gut microbiomes derived from clinical colon biopsies. We combined a rapid peptide search by MSFragger against the Unified Human Gastrointestinal Protein database and the taxonomic and functional analyses with Unipept Desktop and MetaLab-MAG. Across seven samples, we identified and matched nearly 36,000 unique peptides to approximately 300 species and 11 phyla. Unipept Desktop provided gene ontology, InterPro entries, and enzyme commission number annotations, facilitating the identification of relevant metabolic pathways. MetaLab-MAG contributed functional annotations through Clusters of Orthologous Genes and Non-supervised Orthologous Groups categories. These results unveiled functional similarities and differences among the samples. This integrated pipeline holds the potential to provide deeper insights into the taxonomy and functions of the human gut microbiome for interrogating the intricate connections between microbiome balance and diseases.

Item Type:	Article
Additional Information:	Publisher Copyright: © 2024 Wiley-VCH GmbH.
Uncontrolled Keywords:	data processing and analysis,gut microbiome,mass spectrometry,metaproteomics,proteomics,taxonomy,biochemistry,molecular biology,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1303
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	10 Mar 2026 15:30
Last Modified:	15 Mar 2026 07:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102289
DOI:	10.1002/pmic.202400078

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